[BI-2903] Support for program_id in germplasm table

src/main/java/io/swagger/api/germ/GermplasmApi.java

@@ -143,6 +143,7 @@ ResponseEntity<GermplasmListResponse> germplasmGet(
 			@ApiParam(value = "progenyDbId") @Valid @RequestParam(value = "progenyDbId", required = false) String progenyDbId,
 			@ApiParam(value = "commonCropName") @Valid @RequestParam(value = "commonCropName", required = false) String commonCropName,
 			@ApiParam(value = "programDbId") @Valid @RequestParam(value = "programDbId", required = false) String programDbId,
+			@ApiParam(value = "programName") @Valid @RequestParam(value = "programName", required = false) String programName,
 			@ApiParam(value = "externalReferenceID") @Valid @RequestParam(value = "externalReferenceID", required = false) String externalReferenceID,
 			@ApiParam(value = "externalReferenceId") @Valid @RequestParam(value = "externalReferenceId", required = false) String externalReferenceId,
 			@ApiParam(value = "externalReferenceSource") @Valid @RequestParam(value = "externalReferenceSource", required = false) String externalReferenceSource,

src/main/java/io/swagger/model/germ/GermplasmNewRequest.java

@@ -97,6 +97,12 @@ public class GermplasmNewRequest extends BrAPIDataModel {
 	@JsonProperty("taxonIds")
 	private List<TaxonID> taxonIds = null;
 
+	@JsonProperty("programDbId")
+	private String programDbId = null;
+
+	@JsonProperty("programName")
+	private String programName = null;
+
 	public String getBreedingMethodName() {
 		return breedingMethodName;
 	}
@@ -510,6 +516,22 @@ public void setTaxonIds(List<TaxonID> taxonIds) {
 		this.taxonIds = taxonIds;
 	}
 
+	public String getProgramDbId() {
+		return programDbId;
+	}
+
+	public void setProgramDbId(String programDbId) {
+		this.programDbId = programDbId;
+	}
+
+	public String getProgramName() {
+		return programName;
+	}
+
+	public void setProgramName(String programName) {
+		this.programName = programName;
+	}
+
 	@Override
 	public boolean equals(java.lang.Object o) {
 		if (this == o) {
@@ -550,7 +572,9 @@ public boolean equals(java.lang.Object o) {
 				&& Objects.equals(this.subtaxa, germplasmNewRequest.subtaxa)
 				&& Objects.equals(this.subtaxaAuthority, germplasmNewRequest.subtaxaAuthority)
 				&& Objects.equals(this.synonyms, germplasmNewRequest.synonyms)
-				&& Objects.equals(this.taxonIds, germplasmNewRequest.taxonIds);
+				&& Objects.equals(this.taxonIds, germplasmNewRequest.taxonIds)
+				&& Objects.equals(this.programDbId, germplasmNewRequest.programDbId)
+				&& Objects.equals(this.programName, germplasmNewRequest.programName);
 	}
 
 	@Override
@@ -560,7 +584,7 @@ public int hashCode() {
 				countryOfOriginCode, defaultDisplayName, documentationURL, donors, externalReferences, genus,
 				germplasmName, germplasmOrigin, germplasmPUI, germplasmPreprocessing, instituteCode, instituteName,
 				pedigree, seedSource, seedSourceDescription, species, speciesAuthority, storageTypes, subtaxa,
-				subtaxaAuthority, synonyms, taxonIds);
+				subtaxaAuthority, synonyms, taxonIds, programDbId,  programName);
 	}
 
 	@Override
@@ -600,6 +624,8 @@ public String toString() {
 		sb.append("    subtaxaAuthority: ").append(toIndentedString(subtaxaAuthority)).append("\n");
 		sb.append("    synonyms: ").append(toIndentedString(synonyms)).append("\n");
 		sb.append("    taxonIds: ").append(toIndentedString(taxonIds)).append("\n");
+		sb.append("    programDbId: ").append(toIndentedString(programDbId)).append("\n");
+		sb.append("    programName: ").append(toIndentedString(programName)).append("\n");
 		sb.append("}");
 		return sb.toString();
 	}

src/main/java/org/brapi/test/BrAPITestServer/controller/germ/GermplasmApiController.java

@@ -156,6 +156,7 @@ public ResponseEntity<GermplasmListResponse> germplasmGet(
 			@RequestParam(value = "progenyDbId", required = false) String progenyDbId,
 			@RequestParam(value = "commonCropName", required = false) String commonCropName,
 			@RequestParam(value = "programDbId", required = false) String programDbId,
+			@RequestParam(value = "programName", required = false) String programName,
 			@RequestParam(value = "externalReferenceID", required = false) String externalReferenceID,
 			@RequestParam(value = "externalReferenceId", required = false) String externalReferenceId,
 			@RequestParam(value = "externalReferenceSource", required = false) String externalReferenceSource,
@@ -170,7 +171,7 @@ public ResponseEntity<GermplasmListResponse> germplasmGet(
 		Metadata metadata = generateMetaDataTemplate(page, pageSize);
 		List<Germplasm> data = germplasmService.findGermplasm(germplasmPUI, germplasmDbId, germplasmName,
 				accessionNumber, collection, binomialName, genus, species, trialDbId, studyDbId, synonym, parentDbId,
-				progenyDbId, commonCropName, programDbId, externalReferenceId, externalReferenceID,
+				progenyDbId, commonCropName, programDbId, programName, externalReferenceId, externalReferenceID,
 				externalReferenceSource, metadata);
 		return responseOK(new GermplasmListResponse(), new GermplasmListResponseResult(), data, metadata);
 	}

src/main/java/org/brapi/test/BrAPITestServer/model/entity/germ/GermplasmEntity.java

@@ -9,6 +9,7 @@
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
 import org.brapi.test.BrAPITestServer.model.entity.SearchRequestEntity;
 import org.brapi.test.BrAPITestServer.model.entity.core.CropEntity;
+import org.brapi.test.BrAPITestServer.model.entity.core.ProgramEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmInstituteEntity.InstituteTypeEnum;
 import org.brapi.test.BrAPITestServer.model.entity.pheno.ObservationUnitEntity;
 import org.brapi.test.BrAPITestServer.model.entity.pheno.TaxonEntity;
@@ -96,6 +97,8 @@ public class GermplasmEntity extends BrAPIPrimaryEntity {
 	private List<GermplasmStorageTypesEnum> typeOfGermplasmStorageCode;
 	@Column(name = "soft_deleted")
 	private boolean softDeleted;
+    @ManyToOne(cascade = CascadeType.DETACH, fetch = FetchType.LAZY)
+    private ProgramEntity program;
 
     public GermplasmInstituteEntity getHostInstitute() {
         if (getInstitutes() != null) {
@@ -368,4 +371,12 @@ public void setTypeOfGermplasmStorageCode(List<GermplasmStorageTypesEnum> typeOf
 
 	public void setSoftDeleted(boolean sofDeleted) { this.softDeleted = sofDeleted; }
 
+    public ProgramEntity getProgram() {
+        return program;
+    }
+
+    public void setProgram(ProgramEntity program) {
+        this.program = program;
+    }
+
 }

src/main/java/org/brapi/test/BrAPITestServer/service/core/ProgramService.java

@@ -1,9 +1,7 @@
 package org.brapi.test.BrAPITestServer.service.core;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Optional;
-import java.util.UUID;
+import java.util.*;
+import java.util.stream.Collectors;
 
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
@@ -76,14 +74,33 @@ public List<Program> findPrograms(ProgramSearchRequest request, Metadata metadat
 		return programs;
 	}
 
-	public List<ProgramEntity> findByIds(List<String> programDbIds) {
-		var result = new ArrayList<ProgramEntity>();
+	public List<ProgramEntity> findByIds(List<String> programDbIds) throws BrAPIServerException {
+		List<ProgramEntity> result = new ArrayList<>();
 
 		if (programDbIds.isEmpty()) {
 			return result;
 		}
 
-		return programRepository.findByIdIn(programDbIds.stream().map(UUID::fromString).toList());
+		// Dedup programIds by loading into set
+		Set<String> programDbIdSet = new HashSet<>(programDbIds);
+
+		result = programRepository.findByIdIn(programDbIds.stream().map(UUID::fromString).toList());
+
+		if (programDbIdSet.size() != result.size()) {
+			List<String> dbIdsNotFound = new ArrayList<>();
+
+			Set<String> foundDbIds = result.stream().map(pe -> pe.getId().toString()).collect(Collectors.toSet());
+
+			programDbIdSet.forEach(dbId -> {
+				if (!foundDbIds.contains(dbId)) {
+					dbIdsNotFound.add(dbId);
+				}
+			});
+
+			throw new BrAPIServerException(HttpStatus.NOT_FOUND, String.format("The following submitted programDbIds were not found in the db: [%s]", dbIdsNotFound));
+		}
+
+		return result;
 	}
 
 	public Program getProgram(String programDbId) throws BrAPIServerException {

src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java

@@ -4,6 +4,7 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
+import io.swagger.model.core.ProgramSearchRequest;
 import io.swagger.model.germ.*;
 import jakarta.validation.Valid;
 
@@ -12,6 +13,7 @@
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIBaseEntity;
 import org.brapi.test.BrAPITestServer.model.entity.ExternalReferenceEntity;
 import org.brapi.test.BrAPITestServer.model.entity.core.CropEntity;
+import org.brapi.test.BrAPITestServer.model.entity.core.ProgramEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.*;
 import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmInstituteEntity.InstituteTypeEnum;
 import org.brapi.test.BrAPITestServer.model.entity.pheno.TaxonEntity;
@@ -23,6 +25,7 @@
 import org.brapi.test.BrAPITestServer.service.SearchQueryBuilder;
 import org.brapi.test.BrAPITestServer.service.UpdateUtility;
 import org.brapi.test.BrAPITestServer.service.core.CropService;
+import org.brapi.test.BrAPITestServer.service.core.ProgramService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -44,21 +47,23 @@ public class GermplasmService {
 	private final GermplasmDonorRepository donorRepository;
 	private final BreedingMethodService breedingMethodService;
 	private final CropService cropService;
+	private final ProgramService programService;
 
 	@Autowired
 	public GermplasmService(GermplasmRepository germplasmRepository, GermplasmDonorRepository donorRepository,
-			BreedingMethodService breedingMethodService, CropService cropService) {
+	                        BreedingMethodService breedingMethodService, CropService cropService, ProgramService programService) {
 		this.germplasmRepository = germplasmRepository;
 		this.donorRepository = donorRepository;
 
 		this.breedingMethodService = breedingMethodService;
 		this.cropService = cropService;
+		this.programService = programService;
 	}
 
 	public List<Germplasm> findGermplasm(String germplasmPUI, String germplasmDbId, String germplasmName,
 			String accessionNumber, String collection, String binomialName, String genus, String species,
 			String trialDbId, String studyDbId, String synonym, String parentDbId, String progenyDbId,
-			String commonCropName, String programDbId, String externalReferenceId, String externalReferenceID,
+			String commonCropName, String programDbId, String programName, String externalReferenceId, String externalReferenceID,
 			String externalReferenceSource, Metadata metadata)
 		throws BrAPIServerException {
 
@@ -93,6 +98,8 @@ public List<Germplasm> findGermplasm(String germplasmPUI, String germplasmDbId,
 			request.addCommonCropNamesItem(commonCropName);
 		if (programDbId != null)
 			request.addProgramDbIdsItem(programDbId);
+		if (programName != null)
+			request.addProgramNamesItem(programName);
 
 		request.addExternalReferenceItem(externalReferenceId, externalReferenceID, externalReferenceSource);
 
@@ -172,12 +179,10 @@ private SearchQueryBuilder<GermplasmEntity> buildGermplasmSearchQuery(GermplasmS
 				.leftJoinFetch("pedigree", "pedigree")
 				.leftJoinFetch("*pedigree.crossingProject", "crossingProject");
 
-		if (request.getProgramDbIds() != null || request.getProgramNames() != null || request.getTrialDbIds() != null
+		if (request.getTrialDbIds() != null
 				|| request.getTrialNames() != null || request.getStudyDbIds() != null
 				|| request.getStudyNames() != null) {
 			searchQuery = searchQuery.join("observationUnits", "obsunit")
-					.appendList(request.getProgramDbIds(), "*obsunit.program.id")
-					.appendList(request.getProgramNames(), "*obsunit.program.name")
 					.appendList(request.getTrialDbIds(), "*obsunit.trial.id")
 					.appendList(request.getTrialNames(), "*obsunit.trial.name")
 					.appendList(request.getStudyDbIds(), "*obsunit.study.id")
@@ -198,6 +203,7 @@ private SearchQueryBuilder<GermplasmEntity> buildGermplasmSearchQuery(GermplasmS
 				.appendList(request.getGermplasmNames(), "germplasmName")
 				.appendList(request.getGermplasmPUIs(), "germplasmPUI")
 				.appendList(request.getParentDbIds(), "pedigree.parent1.germplasm.id")
+				.appendList(request.getProgramDbIds(), "program.id").appendList(request.getProgramNames(), "program.name")
 				// .appendList(request.getProgenyDbIds(), "*progeny.germplasmDbId")
 				.appendList(request.getGenus(), "genus").appendList(request.getSpecies(), "species")
 				.appendNamesList(request.getBinomialNames(), "genus", "genus", "species")
@@ -529,6 +535,12 @@ private Germplasm convertFromEntity(GermplasmEntity entity) {
 		germ.setCollection(entity.getCollection());
 		if (entity.getCrop() != null)
 			germ.setCommonCropName(entity.getCrop().getCropName());
+
+		if (entity.getProgram() != null) {
+			germ.setProgramDbId(entity.getProgram().getId().toString());
+			germ.setProgramName(entity.getProgram().getName());
+		}
+
 		germ.setCountryOfOriginCode(entity.getCountryOfOriginCode());
 		germ.setDefaultDisplayName(entity.getDefaultDisplayName());
 		germ.setDocumentationURL(entity.getDocumentationURL());
@@ -582,6 +594,11 @@ private List<GermplasmEntity> createEntitiesInBatch(List<GermplasmNewRequest> bo
 				.filter(Objects::nonNull)
 				.collect(Collectors.toSet());
 
+		Set<String> programDbIds = body.stream()
+				.map(GermplasmNewRequest::getProgramDbId)
+				.filter(Objects::nonNull)
+				.collect(Collectors.toSet());
+
 		Map<UUID, BreedingMethodEntity> foundBreedingMethodsById
 				= breedingMethodService.findBreedingMethodsByIds(breedingMethodIds)
 				.stream()
@@ -591,6 +608,11 @@ private List<GermplasmEntity> createEntitiesInBatch(List<GermplasmNewRequest> bo
 				.stream()
 				.collect(Collectors.toMap(CropEntity::getCropName, e -> e));
 
+		Map<UUID, ProgramEntity> foundProgramsByDbId
+				= programService.findByIds(new ArrayList<>(programDbIds))
+				.stream()
+				.collect(Collectors.toMap(ProgramEntity::getId, e -> e));
+
 		for (GermplasmNewRequest request : body) {
 			GermplasmEntity entity = new GermplasmEntity();
 
@@ -605,7 +627,7 @@ private List<GermplasmEntity> createEntitiesInBatch(List<GermplasmNewRequest> bo
 			if (request.getBiologicalStatusOfAccessionCode() != null)
 				entity.setBiologicalStatusOfAccessionCode(request.getBiologicalStatusOfAccessionCode());
 			if (request.getBreedingMethodDbId() != null) {
-				entity.setBreedingMethod(foundBreedingMethodsById.get(request.getBreedingMethodDbId()));
+				entity.setBreedingMethod(foundBreedingMethodsById.get(UUID.fromString(request.getBreedingMethodDbId())));
 			}
 			if (request.getCollection() != null)
 				entity.setCollection(request.getCollection());
@@ -662,6 +684,10 @@ private List<GermplasmEntity> createEntitiesInBatch(List<GermplasmNewRequest> bo
 				updateSynonymEntities(request.getSynonyms(), entity);
 			if (request.getTaxonIds() != null)
 				updateTaxonEntities(request.getTaxonIds(), entity);
+			if (request.getProgramDbId() != null) {
+				ProgramEntity program = foundProgramsByDbId.get(UUID.fromString(request.getProgramDbId()));
+				entity.setProgram(program);
+			}
 
 			toSave.add(entity);
 		}
@@ -739,6 +765,10 @@ private void updateEntity(GermplasmEntity entity, GermplasmNewRequest request) t
 			updateSynonymEntities(request.getSynonyms(), entity);
 		if (request.getTaxonIds() != null)
 			updateTaxonEntities(request.getTaxonIds(), entity);
+		if (request.getProgramDbId() != null) {
+			ProgramEntity program = programService.getProgramEntity(request.getProgramDbId());
+			entity.setProgram(program);
+		}
 	}
 
 	private void updateTaxonEntities(List<TaxonID> taxonIds, GermplasmEntity entity) {

src/main/resources/db/migration/V006_003__add_program_id_to_germplasm_and_migrate.sql

@@ -0,0 +1,40 @@
+ALTER TABLE germplasm
+ADD COLUMN program_id UUID;
+
+ALTER TABLE germplasm
+ADD CONSTRAINT germplasm_program_fk
+    FOREIGN KEY (program_id)
+    REFERENCES public.program(id);
+
+CREATE INDEX germplasm_program_idx ON germplasm (program_id, id);
+
+UPDATE germplasm set program_id = pquery.program_id
+FROM (
+    SELECT g.id AS germplasm_id, p.id AS program_id
+    FROM germplasm g
+             JOIN germplasm_external_references gex ON g.id = gex.germplasm_entity_id
+             JOIN external_reference ex ON ex.id = gex.external_references_id
+             JOIN external_reference ex2 ON ex2.external_reference_id = ex.external_reference_id
+             JOIN program_external_references pex ON pex.external_references_id = ex2.id
+             JOIN program p ON p.id = pex.program_entity_id
+    WHERE ex.external_reference_source = 'breedinginsight.org/programs' AND ex2.external_reference_source = 'breedinginsight.org') pquery
+WHERE id = pquery.germplasm_id;
+
+-- Assertion to ensure all germplasm are now associated with a program
+DO $$
+    DECLARE
+        germs_without_program_count integer;
+
+    BEGIN
+        SELECT COUNT(*)
+        INTO germs_without_program_count
+        FROM germplasm g
+        WHERE g.program_id IS NULL;
+
+        IF germs_without_program_count <> 0 THEN
+                RAISE EXCEPTION
+                    'V006.003 After migration, expected all germplasm rows to have program_id set, but there are % rows with program_id not set',
+                    germs_without_program_count;
+        END IF;
+    END
+$$;